Modomics - A Database of RNA Modifications

ID Card:

Full name: Methylenetetrahydrofolate--tRNA-(uracil-54-)-methyltransferase TrmFO
Synonym: Gid, YlyC
GI: 3183519
Orf: BSU16130
COG: COG1206
UniProt: P39815
Alpha Fold Predicted Structure: AF-P39815-F1
Enzyme type: methyltransferase
Position of modification - modification: t:54 - m5U



Protein sequence:

MNQQTVNVIGAGLAGSEAAWQLAKRGIQVKLYEMRPVKQTPAHHTDKFAELVCSNSLRSNTLANAVGVLKEEMRALDSAIIAAADECSVPAGGALAVDRHEFAASVTNRVKNHPNVTVINEEVTEIPEGPTIIATGPLTSESLSAQLKELTGEDYLYFYDAAAPIVEKDSLDMDKVYLKSRYDKGEAAYLNCPMTEEEFDRFHEALTSAETVPLKEFEKEIFFEGCMPIEVMAKRGKKTMLFGPMKPVGLEHPVTGKRPYAVVQLRQDDAAGTLYNIVGFQTHLKWGDQKEVLKLIPGLENVEIVRYGVMHRNTFINSPSLLKPTYQFKNRSDLFFAGQMTGVEGYVESAASGLVAGINAAKLVLGEELVIFPQETAIGSMAHYITTTNQKNFQPMNANFGLLKELPVKIKNKKERNEQYANRAIETIQTISKTI

Comments:

In all Eukarya and many Gram-negative Bacteria, the methyl donor for this reaction is S-adenosyl-L-methionine (S-AdoMet), while in several Gram-positive Bacteria, the source of carbon is N5, N10-methylenetetrahydrofolate (CH2H4folate) . Modification in position 54 has been mapped in all tRNAs( Urbonavičius et al. 2005). Enzymatic reactions has been mapped to the MODOMICS RNA dataset. Therefore, more tRNA isoacepptors could be available.




Reaction Substrate SubstrateType Position (Anti)Codon Modified (Anti)Codon Amino Acid Change Transcript Name Transcript Region Cellular Localization References
U:m5U RNA tRNA 54
U:m5U RNA tRNA 54 UGC UGC tRNAAlaUGC TΨC-loop Prokaryotic Cytosol
U:m5U RNA tRNA 54 GGC GGC tRNAAlaGGC TΨC-loop Prokaryotic Cytosol
U:m5U RNA tRNA 54 ICG ICG tRNAArgICG TΨC-loop Prokaryotic Cytosol
U:m5U RNA tRNA 54 UCU UCU tRNAArgUCU TΨC-loop Prokaryotic Cytosol
U:m5U RNA tRNA 54 CCU CCU tRNAArgCCU TΨC-loop Prokaryotic Cytosol
U:m5U RNA tRNA 54 CCG CCG tRNAArgCCG TΨC-loop Prokaryotic Cytosol
U:m5U RNA tRNA 54 GCC GCC tRNAGlyGCC TΨC-loop Prokaryotic Cytosol
U:m5U RNA tRNA 54 !CC !CC tRNAGly!CC TΨC-loop Prokaryotic Cytosol
U:m5U RNA tRNA 54 }AU }AU tRNAIle}AU TΨC-loop Prokaryotic Cytosol
U:m5U RNA tRNA 54 CAG CAG tRNALeuCAG TΨC-loop Prokaryotic Cytosol
U:m5U RNA tRNA 54 UAG UAG tRNALeuUAG TΨC-loop Cytoplasm
U:m5U RNA tRNA 54 $UU $UU tRNALys$UU TΨC-loop Prokaryotic Cytosol
U:m5U RNA tRNA 54 CAU CAU tRNAMetCAU TΨC-loop Prokaryotic Cytosol
U:m5U RNA tRNA 54 #AA #AA tRNAPhe#AA TΨC-loop Prokaryotic Cytosol
U:m5U RNA tRNA 54 5GG 5GG tRNAPro5GG TΨC-loop Prokaryotic Cytosol
U:m5U RNA tRNA 54 GCU GCU tRNASerGCU TΨC-loop Prokaryotic Cytosol
U:m5U RNA tRNA 54 5GA 5GA tRNASer5GA TΨC-loop Prokaryotic Cytosol
U:m5U RNA tRNA 54 GGA GGA tRNASerGGA TΨC-loop Prokaryotic Cytosol
U:m5U RNA tRNA 54 5GU 5GU tRNAThr5GU TΨC-loop Prokaryotic Cytosol
U:m5U RNA tRNA 54 CCA CCA tRNATrpCCA TΨC-loop Prokaryotic Cytosol
U:m5U RNA tRNA 54 QUA QUA tRNATyrQUA TΨC-loop Prokaryotic Cytosol
U:m5U RNA tRNA 54 5AC 5AC tRNAVal5AC TΨC-loop Prokaryotic Cytosol
U:m5U RNA tRNA 54 GAC GAC tRNAValGAC TΨC-loop Prokaryotic Cytosol
U:m5U RNA tRNA 54 CAU CAU tRNAIniCAU TΨC-loop Prokaryotic Cytosol

Alpha Fold Predicted Structure:






Clear Selection and Reset Camera

Protein sequence:

M N Q Q T V N V I G A G L A G S E A A W Q L A K R G I Q V K L Y E M R P V K Q T P A H H T D K F A E L V C S N S L R S N T L A N A V G V L K E E M R A L D S A I I A A A D E C S V P A G G A L A V D R H E F A A S V T N R V K N H P N V T V I N E E V T E I P E G P T I I A T G P L T S E S L S A Q L K E L T G E D Y L Y F Y D A A A P I V E K D S L D M D K V Y L K S R Y D K G E A A Y L N C P M T E E E F D R F H E A L T S A E T V P L K E F E K E I F F E G C M P I E V M A K R G K K T M L F G P M K P V G L E H P V T G K R P Y A V V Q L R Q D D A A G T L Y N I V G F Q T H L K W G D Q K E V L K L I P G L E N V E I V R Y G V M H R N T F I N S P S L L K P T Y Q F K N R S D L F F A G Q M T G V E G Y V E S A A S G L V A G I N A A K L V L G E E L V I F P Q E T A I G S M A H Y I T T T N Q K N F Q P M N A N F G L L K E L P V K I K N K K E R N E Q Y A N R A I E T I Q T I S K T I

Secondary Structure Alphabet

  • G: 3-turn helix (310helix)
  • H: α-helix
  • I: 𝝅-helix (5 - turn helix)
  • T: Hydrogen Bonded Turn
  • B: β-sheet
  • S: Bend
  • C: Coil (residues not present in any of the above conformations)
  • N: Not assigned

Download PDB Structures & DSSP Secondary Structures:

Alpha Fold Pdb Files   AF-P39815-F1.pdb  
Alpha Fold Pdbx/mmCIF Files   AF-P39815-F1.cif  
DSSP Secondary Structures   P39815.dssp  





Publications:

Title Authors Journal Details PubMed Id DOI
Identification of a novel gene encoding a flavin-dependent tRNA:m5U methyltransferase in bacteria--evolutionary implications. Urbonavicius J, Skouloubris S, Myllykallio H, Grosjean H Nucleic Acids Res [details] 16027442 -
Insights into folate/FAD-dependent tRNA methyltransferase mechanism: role of two highly conserved cysteines in catalysis. Hamdane D, Argentini M, Cornu D, Myllykallio H, Skouloubris S, Hui-Bon-Hoa G, Golinelli-Pimpaneau B J Biol Chem [details] 21846722 -
A catalytic intermediate and several flavin redox states stabilized by folate-dependent tRNA methyltransferase from Bacillus subtilis. Hamdane D, Guerineau V, Un S, Golinelli-Pimpaneau B Biochemistry [details] 21561081 -
Expression and purification of untagged and histidine-tagged folate-dependent tRNA:m5U54 methyltransferase from Bacillus subtilis. Hamdane D, Skouloubris S, Myllykallio H, Golinelli-Pimpaneau B Protein Expr Purif [details] 20412857 -
FAD/Folate-Dependent tRNA Methyltransferase: Flavin as a new methyl-transfer agent. Hamdane D, Argentini M, Cornu D, Golinelli-Pimpaneau B, Fontecave M... J Am Chem Soc [details] 23157377 -

Links:

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